R3D Align

R3D Align Web Server: Global Nucleotide-Level RNA 3D Structural Alignment

R3D Align Web Server makes global nucleotide-to-nucleotide alignments of RNA three-dimensional (3D) structures to enable detailed structural comparison and evolutionary analysis at single-nucleotide resolution.

Key Features:

• Nucleotide-Level Structural Alignment: Computes precise global alignments between RNA 3D structures at the nucleotide level for comparative structural analysis.
• Precomputed Ribosomal RNA Alignments: Provides access to precomputed alignments of large RNA 3D structures, including all ribosomal RNAs.
• Non-Redundant RNA 3D Structure Access: Integrates curated non-redundant RNA 3D structure sets, including equivalence class structure files and best-modeled representative structures from each group.
• Comprehensive Alignment Output: Generates detailed structural alignment results to support interpretation of nucleotide correspondences and structural relationships.

Scientific Applications:

• RNA Structural and Evolutionary Analysis: Identifies structural similarities and differences among RNA molecules to investigate RNA function, interactions, and evolutionary relationships.

Methodology:

R3D Align accesses curated non-redundant RNA 3D structure datasets and applies global nucleotide-to-nucleotide structural alignment algorithms to compute accurate structural correspondences between RNA molecules, including large ribosomal RNAs, using representative equivalence class models for high-quality comparative analysis.